RNA-Decoder is the first comparative method, which explicitly takes
the known protein-coding context of an RNA-sequence alignment into account in
order to predict evolutionarily conserved secondary-structure elements, which
may span both coding and non-coding regions. On known secondary structures,
RNA-Decoder shows a sensitivity similar to the programs Mfold, Pfold and
RNAalifold. When scanning the entire genomes of HCV and polio virus for
structure elements, RNA-Decoder's results indicate a markedly higher
specificity than Mfold, Pfold and RNAalifold

Input Multiple Sequence Alignment (with optional annotation)

Paste a multiple sequence alignment of one or more sequences in FASTA format (up to 200kb total). An optional annotation can be provided, which should be a FASTA entry consisting of 1, 2, and 3 to indicate codon positions (or just 3 for non-coding regions). Click for example

Paste a multiple sequence alignment of one or more sequences in FASTA format, species should match those in target alignment.

Prediction Mode

Choose mode RNA-Decoder should run in:

Fold acts like a normal RNA secondary structure predictor, giving a single set of mutually compatible basepairs.Scan will predict the probability of each positions being basepaired.
Note: For efficiency the input will be split into 600 bps side windows, created by sliding 200 bps each time for both modes.